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The pH of soil in terrestrial environments or of water in aquatic ones is a condition that can exert a powerful influence on the distribution and abundance of organisms. The protoplasm of the root cells of most vascular plants is damaged as a direct result of toxic concentrations of H⁺ or OH⁻ ions in soils below pH 3 or above pH 9, respectively. Further, indirect effects occur because soil pH influences the availability of nutrients and/or the concentration of toxins.

Increased acidity (low pH) may act in three ways: (i) directly, by upsetting osmoregulation, enzyme activity or gaseous exchange across respiratory surfaces; (ii) indirectly, by increasing the concentration of toxic heavy metals at higher pHs, particularly aluminium (Al³⁺) but also manganese (Mn²⁺) and iron (Fe³⁺), which are essential plant nutrients; and (iii) indirectly, by reducing the quality and range of food sources available to animals. Tolerance limits for pH vary amongst plant species, but only a minority are able to grow and reproduce at a pH below about 4.5.

In alkaline soils, iron (Fe³⁺) and phosphate (), and certain trace elements such as manganese (Mn²⁺), are fixed in relatively insoluble compounds, and plants may then suffer because there is too little rather than too much of them. For example, calcifuge plants (those characteristic of acid soils) commonly show symptoms of iron deficiency when they are transplanted to more alkaline soils. In general, however, soils and waters with a pH above 7 tend to be hospitable to many more species than those that are more acid. Chalk and limestone grasslands carry a much richer flora (and associated fauna) than acid grasslands and the situation is similar for animals inhabiting streams, ponds and lakes.

Some Archaea can tolerate and even grow best in environments with a pH far outside the range tolerated by eukaryotes. Such environments are rare, but occur in volcanic lakes and geothermal springs where they are dominated by sulphur‐oxidising bacteria whose pH optima lie between 2 and 4 and which cannot grow at neutrality (Stolp, 1988). Thiobacillus ferroxidans occurs in the waste from industrial metal‐leaching processes and tolerates pH 1; T. thiooxidans cannot only tolerate but can grow at pH 0. Towards the other end of the pH range are the alkaline environments of soda lakes with pH values of 9–11, which are inhabited by cyanobacteria such as Anabaenopsis arnoldii and Spirulina platensis.